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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Uncovering the re-distribution mechanism of Ni in a de-alloyed Ni-Cr alloy in molten fluorinated salts

A mechanism of Ni redeposition during dealloying corrosion of Ni-Cr is investigated. A model Ni20Cr (wt%) metal alloy was exposed to molten LiF-NaF-KF eutectic (FLiNaK) at 600 °C and at an applied potential of +2.1 VK+/K, above the critical potential for onset of dealloying. Upon extended exposure times (up to 12 h), prominent salt-filled corrosion channels emerge along grain boundaries. A unique grain boundary corrosion mechanism, with respect to the exposed faces of the grains, a central focus of this investigation, is intrinsically connected to the formation of high purity Ni-rich de-alloyed regions within the salt-filled channel. We implement microscale techniques such as energy dispersive spectroscopy (EDS) and electron backscatter diffraction (EBSD) to uncover morphological and compositional variations in relevance to the formation of bicontinuous porosity from corrosion dealloying. To rationalize our findings, a phase-field model is developed and discovers a mechanism in which dissolved Ni from one grain can be redeposited on an adjacent grain at a given difference in interfacial energies. The interaction of chemical and structural factors at the grain boundaries plays a central role in elucidating the dynamics of this phenomenon and its implications towards corrosion.

Mills, Sean H↗
DOE OSTI2020

Genomic analyses implicate noncoding de novo variants in congenital heart disease

A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10 -4 ). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10 -5 ). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10 -3 ). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10 -5 ). Overall, our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

De novo design of proteins housing excitonically coupled chlorophyll special pairs

Natural photosystems couple light harvesting to charge separation using a ‘special pair’ of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C 2 -symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

De novo design of buttressed loops for sculpting protein functions

In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9–14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

De novo design of obligate ABC-type heterotrimeric proteins

The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the assembly of higher-order branching structures is an important challenge for protein design. We designed helical heterotrimers with specificity conferred by buried hydrogen bond networks and large aromatic residues to enhance shape complementary packing. We obtained ten designs for which all three chains cooperatively assembled into heterotrimers with few or no other species present. Crystal structures of a helical bundle heterotrimer and extended versions, with helical repeat proteins fused to individual subunits, showed all three chains assembling in the designed orientation. We used these heterotrimers as building blocks to construct larger cyclic oligomers, which were structurally validated by electron microscopy. Our three-way junction designs provide new routes to complex protein nanostructures and enable the scaffolding of three distinct ligands for modulation of cell signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

De novo fabrication of multi-heteroatom-doped carbonaceous materials via an in situ doping strategy

Finding a succinct strategy to fabricate multi-heteroatom-doped nanoporous carbonaceous materials is a long-term challenge and highly desired research topic. The key to success is the rational design of easy to obtain and functionalized precursors. Herein, de novo fabrication of carbonaceous materials doped with multiple heteroatoms namely boron, nitrogen, oxygen, fluorine, and sulfur was achieved via a one-step in situ doping procedure using task-specific ionic liquids (TSILs) as precursors. Our strategy hinges on the adoption of particularly designed TSILs with structures functionalized with (1) boron source-containing anions, (2) imidazolium functionalities as the carbon and nitrogen source, (3) nitrile groups capable of trimerization during the heating process, and (4) bis(trifluoromethanesulphonyl)imide and related anions performing as the source of heteroatoms (i.e., fluorine, nitrogen, sulfur, and oxygen) and porogens. The unique structures of the as-prepared TSILs make them qualified precursors for the production of multi-heteroatom-doped carbonaceous materials through simple thermal treatment, with surface areas up to 1021 m 2 g -1 . The introduction of multiple heteroatoms provides the carbonaceous materials with efficient adsorption performance for the capture of hazardous anionic pollutants, dyes, and neutral organic molecules. This finding expands the versatility of TSILs with multi-functionalized architectures, delivering nanoporous materials with wide applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Alignment of Au nanorods along de novo designed protein nanofibers studied with automated image analysis

In this paper, we focus on exploring the directional assembly of anisotropic Au nanorods along de novo designed 1D protein nanofiber templates. Using machine learning and automated image processing, we analyze scanning electron microscopy (SEM) images to study how the attachment density and alignment fidelity are influenced by variables such as the aspect ratio of the Au nanorods, and the salt concentration of the solution. We find that the Au nanorods prefer to align parallel to the protein nanofibers. This preference decreases with increasing salt concentration, but is only weakly sensitive to the nanorod aspect ratio. While the overall specific Au nanorod attachment density to the protein fibers increases with increasing solution ionic strength, this increase is dominated primarily by non-specific binding to the substrate background, and we find that greater specific attachment (nanorods attached to the nanofiber template as compared to the substrates) occurs at the lower studied salt concentrations, with the maximum ratio of specific to non-specific binding occurring when the protein fiber solutions are prepared in 75 mM NaCl concentration.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A forced Korteweg–de Vries model for nonlinear mixing of oscillations in a dusty plasma

Nonlinear mixing of oscillations in a dusty plasma due to the harmonic time varying modulation of a nonlinear compressional oscillation is analyzed using a simple mathematical model consisting of a forced Korteweg-de Vries equation. An exact analytic solution of this equation is found to exhibit nonlinear mixing in the system. Here, the model solution can be usefully employed to predict the existence of nonlinear mixing of oscillations in a two-dimensional dusty plasma system of a particular experimental configuration.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

2nd and 3rd order spectral energy corrections with penumbral de-blurring methodology for opacity platform used on the National Ignition Facility

The Opacity Spectrometer (OpSpec) used in the National Ignition Facility’s opacity experiments measures x-ray spectra from 0.9 to 2.1 keV from the different experimental regions: the backlight source, emission source, and the absorption region with the transmission calculated from these regions. The OpSpec designs have gone through several iterations to help improve the signal-to-noise ratio, remove alternate crystal plane reflections, and improve spectral resolution, which helps to increase the validity of the opacity measurements. However, the source spans well outside the current working spectral range, and higher-order reflections are intrinsic to the crystal, which increases the overall signal seen in the data regions. The recorded data are the convolution of 1st order transmission, higher-order reflections, and the penumbra blurring. In conclusion, this work represents the details for deconvolving the 2nd and 3rd order spectral energy corrections with a penumbral de-blurring to correct the relative measurement of x-ray intensity of different spectral energies and further analysis of datasets relevant to the opacity experiments.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

De novo designed protein inhibitors of amyloid aggregation and seeding

Neurodegenerative diseases are characterized by the pathologic accumulation of aggregated proteins. Known as amyloid, these fibrillar aggregates include proteins such as tau and amyloid-β (Aβ) in Alzheimer’s disease (AD) and alpha-synuclein (αSyn) in Parkinson’s disease (PD). The development and spread of amyloid fibrils within the brain correlates with disease onset and progression, and inhibiting amyloid formation is a possible route toward therapeutic development. Recent advances have enabled the determination of amyloid fibril structures to atomic-level resolution, improving the possibility of structure-based inhibitor design. In this work, we use these amyloid structures to design inhibitors that bind to the ends of fibrils, “capping” them so as to prevent further growth. Using de novo protein design, we develop a library of miniprotein inhibitors of 35 to 48 residues that target the amyloid structures of tau, Aβ, and αSyn. Biophysical characterization of top in silico designed inhibitors shows they form stable folds, have no sequence similarity to naturally occurring proteins, and specifically prevent the aggregation of their targeted amyloid-prone proteins in vitro. The inhibitors also prevent the seeded aggregation and toxicity of fibrils in cells. In vivo evaluation reveals their ability to reduce aggregation and rescue motor deficits in Caenorhabditis elegans models of PD and AD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

De novo design of small beta barrel proteins

Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy–based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

De novo design of D-peptide ligands: Application to influenza virus hemagglutinin

D-peptides hold great promise as therapeutics by alleviating the challenges of metabolic stability and immunogenicity in L-peptides. However, current D-peptide discovery methods are severely limited by specific size, structure, and the chemical synthesizability of their protein targets. Here, we describe a computational method for de novo design of D-peptides that bind to an epitope of interest on the target protein using Rosetta’s hotspot-centric approach. The approach comprises identifying hotspot sidechains in a functional protein–protein interaction and grafting these side chains onto much smaller structured peptide scaffolds of opposite chirality. The approach enables more facile design of D-peptides and its applicability is demonstrated by design of D-peptidic binders of influenza A virus hemagglutinin, resulting in identification of multiple D-peptide lead series. The X-ray structure of one of the leads at 2.38 Å resolution verifies the validity of the approach. This method should be generally applicable to targets with detailed structural information, independent of molecular size, and accelerate development of stable, peptide-based therapeutics.

Science & Technology - Other Topics↗
DOE OSTI2021

A multispecies turbulence model for the mixing and de-mixing of miscible fluids

A de-mix capable model for turbulence in compressible, variable density flows is proposed. The model is based on the Besnard-Harlow-Rauenzahn (BHR) family of models (Besnard D, Harlow F, Rauenzahn R, et al. Turbulence transport equations for variable-density turbulence and their relationship to two-field models. NM (United States): Los Alamos National Laboratory; 1992 (Technical Report LA-12303-MS), but is extended to track the evolution of the turbulent fluxes and fluctuations in the material mass fractions for each species present. The new evolution equations are introduced without requiring additional closures or new empirically tuned coefficients relative to previous BHR models, and are shown to improve the model’s ability to reproduce the behaviour of simulations containing mixing layers that are constrained by a stabilising force. As a result, the model is tested in a range of canonical flows including Rayleigh-Taylor driven, shock driven, and shear driven turbulence, and is shown to produce reasonable agreement with simulations and experiments in these scenarios.

42 ENGINEERING↗
DOE OSTI2021

Fermi surfaces of the topological semimetal CaSn 3 probed through de Haas van Alphen oscillations

Abstract In the search of topological superconductors, nailing down the Fermiology of the normal state is as crucial a prerequisite as unraveling the superconducting pairing symmetry. In particular, the number of time-reversal-invariant momenta (TRIM) in the Brillouin zone enclosed by Fermi surfaces is closely linked to the topological class of time-reversal-invariant systems, and can experimentally be investigated. We report here a detailed study of de Haas van Alphen quantum oscillations in single crystals of the topological semimetal CaSn 3 with torque magnetometry in high magnetic fields up to 35 T. In conjunction with density functional theory based calculations, the observed quantum oscillations frequencies indicate that the Fermi surfaces of CaSn 3 enclose an odd number of TRIM, satisfying one of the proposed criteria to realize topological superconductivity. Nonzero Berry phases extracted from the magnetic oscillations also support the nontrivial topological nature of CaSn 3 .

Physics↗
DOE OSTI2021

Redshift space power spectrum beyond Einstein-de Sitter kernels

Abstract We develop a framework to compute the redshift space power spectrum (PS), with kernels beyond Einstein-de Sitter (EdS), that can be applied to a wide variety of generalized cosmologies. We build upon a formalism that was recently employed for standard cosmology in Chen, Vlah & White (2020), and utilize an expansion of the density-weighted velocity moment generating function that explicitly separates the magnitude of the k-modes and their angle to the line-of-sight direction dependencies. We compute the PS for matter and biased tracers to 1-loop Perturbation Theory (PT) and show that the expansion has a correct infrared and ultraviolet behavior, free of unwanted divergences. We also add Effective Field Theory (EFT) counterterms, necessary to account for small-scale contributions to PT, and employ an IR-resummation prescription to properly model the smearing of the BAO due to large scale bulk flows within Standard-PT. To demonstrate the applicability of our formalism, we apply it on the ΛCDM and the Hu-Sawicki f(R) models, and compare our numerical results against the elephant suite of N-body simulations, finding very good agreement up to k = 0.27 Mpc -1 h at z = 0.5 for the first three non-vanishing Legendre multipoles of the PS. To our knowledge, the model presented in this work is the most accurate theoretical EFT-PT for modified gravity to date, being the only one that accounts for beyond linear local biasing in redshift-space. Hence, we argue our RSD modeling is a promising tool to construct theoretical templates in order to test deviations from ΛCDM using real data obtained from the next stage of cosmological surveys such as DESI and LSST.

Astronomy & Astrophysics↗
DOE OSTI2024

De-Higgsing in eleven-dimensional supergravity on the squashed S 7

Abstract In this paper we construct the subset of modes onS 7 that are relevant in the compactification of eleven-dimensional supergravity on a squashedS 7 when restricted to the sector that comprises singlets under the S p ( 1 ) × S p ( 2 ) isometry of the squashed sphere. Some of the properties of these modes, connected to the transition from the roundS 7 to the squashedS 7 , are analysed in detail. Special features of the Rarita–Schwinger operator, described in earlier work by Buchdahl, are explained and related to properties of the squashedS 7 operator spectrum obtained in previous work by the authors. We then discuss how the singlet modes give rise to supermultiplets in the left-squashed case, the phenomenon of de-Higgsing, and what happens to the AdS 4 fields in these supermultiplets under an orientation reversal (‘skew-whiffing’) of the squashedS 7 . Finally, we consider the possible choices of boundary conditions that appear for some of these fields in AdS 4 in the case of the right-squashed non-supersymmetric compactification, and how these choices may affect the stability of the gravity theory.

Physics↗